2016 BIML lecture 
B3. Network Modeling and Analysis for Data-driven Biology
Generating biological hypothesis based on gene networks

3 scripts for analysis
CAH_find.py : a script to find context-associated hubs
GBA_predict_genes.py : predict candidate genes from guide genes
GBA_predict_func.py : predict a function of a gene by direct-neighborhood

5 input files
GO_terms.txt : list of genes and corresponding GOterms
hublist : list of hub genes in the network
Test_network_3int.nw : network used for analysis. integrated 3 sets
guidegenes.txt : list of guide genes to predict candidate genes
- Mus musculus Innate immune response genes. From GO:0045087
DEGs.txt : list of differentially expressed genes
- upregulated genes from Yang S. et al., Immune defense is the primary function associated with the differentially expressed genes in the cochlea following acoustic trauma, Hearing Research (2015)
